Question: Galaxy Passing An Incorrect Directory To A Script...
9.1 years ago by
Nick Schurch • 50
Nick Schurch • 50 wrote:
I'm having a problem with a script in galaxy. In the xml config file for the tool I have an html output file defined by <outputs> <data name="webpageout" format="html"/> </outputs> I then use $webpageout.files_path to pass to the script the location where galaxy is putting the files the script creates. My webpage contains a link for downloading a postscript file that is created by the script and the correct path is needed or the download link doesn't work. Here at Dundee University we have a 'development' galaxy install and a 'live' galaxy install. Both are the same version and run off the same mysql database. When I run the script on the 'develpment' version the script works fine - $webpageout.files_path passes the correct directory to the script and the script can manipulate the file and link to it correctly. Unfortunately, when run on the 'live' version the script throws an error. It appears that galaxy is passing the script an incorrect directory path through $webpageout.files_path. The path it passes the script looks something like /galaxy_live/database/job_working_directory/604/dataset_615_files, but when I look for the files manually they are actually in /galaxy_live/database/files/000/dataset_615_files/ . Does anyone have any idea why galaxy would pass a 'working directory' to the script rather than the directory where the files are actually stored? Is it that galaxy actually creates the files in the working directory and then moves them? I'm also really confused as to why the 'development' installation works fine, but the 'live' installation throws this error. Any insight would be greatly appreciated. -- Cheers, Nick Schurch Data Analysis Group (The Barton Group), School of Life Sciences, University of Dundee, Dow St, Dundee, DD1 5EH, Scotland, UK Tel: +44 1382 388707 Fax: +44 1382 345 893
ADD COMMENT • link •